Structure of PDB 3b4y Chain B Binding Site BS01

Receptor Information
>3b4y Chain B (length=332) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ELKLGYKASAEQFAPRELVELAVAAEAHGMDSATVSDHFQPWRHQGGHAP
FSLSWMTAVGERTNRLLLGTSVLTPTFRYNPAVIAQAFATMGCLYPNRVF
LGVGTGEALNEIATGYEGAWPEFKERFARLRESVGLMRQLWSGDRVDFDG
DYYRLKGASIYDVPDGGVPVYIAAGGPAVAKYAGRAGDGFICTSGKGEEL
YTEKLMPAVREGAAAADRSVDGIDKMIEIKISYDPDPELAMNNTRFWAPL
SLTAEQKHSIDDPIEMEKAADALPIEQIAKRWIVASDPDEAVEKVGQYVT
WGLNHLVFHAPGHDQRRFLELFQSDLAPRLRR
Ligand information
Ligand IDF42
InChIInChI=1S/C29H36N5O18P/c1-12(25(42)31-17(28(46)47)4-6-21(38)30-16(27(44)45)5-7-22(39)40)52-53(49,50)51-11-20(37)23(41)19(36)10-34-18-9-14(35)3-2-13(18)8-15-24(34)32-29(48)33-26(15)43/h2-3,8-9,12,16-17,19-20,23,35-37,41H,4-7,10-11H2,1H3,(H,30,38)(H,31,42)(H,39,40)(H,44,45)(H,46,47)(H,49,50)(H,33,43,48)/t12-,16-,17-,19-,20+,23-/m0/s1
InChIKeyGEHSZWRGPHDXJO-NALJQGANSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[CH](O[P](O)(=O)OC[CH](O)[CH](O)[CH](O)CN1c2cc(O)ccc2C=C3C(=O)NC(=O)N=C13)C(=O)N[CH](CCC(=O)N[CH](CCC(O)=O)C(O)=O)C(O)=O
OpenEye OEToolkits 1.7.5C[C@@H](C(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=O)O)O[P@](=O)(O)OC[C@H]([C@H]([C@H](CN1c2cc(ccc2C=C3C1=NC(=O)NC3=O)O)O)O)O
OpenEye OEToolkits 1.7.5CC(C(=O)NC(CCC(=O)NC(CCC(=O)O)C(=O)O)C(=O)O)OP(=O)(O)OCC(C(C(CN1c2cc(ccc2C=C3C1=NC(=O)NC3=O)O)O)O)O
CACTVS 3.385C[C@H](O[P](O)(=O)OC[C@@H](O)[C@@H](O)[C@@H](O)CN1c2cc(O)ccc2C=C3C(=O)NC(=O)N=C13)C(=O)N[C@@H](CCC(=O)N[C@@H](CCC(O)=O)C(O)=O)C(O)=O
ACDLabs 10.04O=C(O)C(NC(=O)CCC(C(=O)O)NC(=O)C(OP(=O)(O)OCC(O)C(O)C(O)CN3c1c(ccc(O)c1)C=C2C3=NC(=O)NC2=O)C)CCC(=O)O
FormulaC29 H36 N5 O18 P
NameCOENZYME F420
ChEMBL
DrugBankDB03913
ZINCZINC000198210272
PDB chain3b4y Chain B Residue 338 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3b4y Crystal structures of F420-dependent glucose-6-phosphate dehydrogenase FGD1 involved in the activation of the anti-tuberculosis drug candidate PA-824 reveal the basis of coenzyme and substrate binding
Resolution1.95 Å
Binding residue
(original residue number in PDB)		S38 D39 H40 S73 V74 T76 T107 G108 E109 F125 A175 G177 G178 P179 A180 V181 T195 H260
Binding residue
(residue number reindexed from 1)		S36 D37 H38 S71 V72 T74 T105 G106 E107 F123 A173 G175 G176 P177 A178 V179 T193 H258
Annotation score1
Binding affinityMOAD: Kd=4.5uM
Enzymatic activity
Catalytic site (original residue number in PDB) M32 H40 W44 E109
Catalytic site (residue number reindexed from 1) M30 H38 W42 E107
Enzyme Commision number 1.1.98.2: glucose-6-phosphate dehydrogenase (coenzyme-F420).
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0052749 glucose-6-phosphate dehydrogenase (coenzyme F420) activity
GO:0070967 coenzyme F420 binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0045454 cell redox homeostasis
Cellular Component
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0009274 peptidoglycan-based cell wall

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3b4y, PDBe:3b4y, PDBj:3b4y
PDBsum3b4y
PubMed18434308
UniProtP9WNE1|FGD_MYCTU F420-dependent glucose-6-phosphate dehydrogenase (Gene Name=fgd1)

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